An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair.
The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA).
Srikanta
Deepa
D
Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.
Sen
Shurjo K
SK
Huang
Charles T
CT
Conlin
Erin M
EM
Rhodes
Ryan M
RM
Batzer
Mark A
MA
D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D019295:Computational Biology; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D015894:Genome, Human; D006801:Humans; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D002679:Pan troglodytes; D018626:Retroelements / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D018626:Retroelements